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C-CoMP-STC / GEM-mit1002

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Why is MEMOTE giving a different number of reactions than KBase #40

Closed hgscott closed 7 months ago

hgscott commented 8 months ago

When I look at the report I KBase, I see that there are 1216 reactions: Image

But when I generate a MEMOTE report, the report says that there are 1301 reactions, which includes exchange reactions: Image

hgscott commented 8 months ago

I loaded the model in COBRA (locally, in my memote-test conda environment), and checked the number of reactions, and got the same as MEMOTE: Image

hgscott commented 8 months ago

I think KBase just classified some reactions differently and so is only counting what it considers a "reaction".

Like I don't think they are counting exchange reactions. If you inspect the model in KBase and try to search for exchange reactions, none show up: Image

But that app is also saying that there are 1,239 total reactions, which is different than what the report says.

hgscott commented 8 months ago

Daniel says to open an ticket with KBase to get clarification.